Effect of Halogen Substitutions on dUMP to Stability of Thymidylate Synthase/dUMP/mTHF Ternary Complex Using Molecular Dynamics Simulation
暂无分享,去创建一个
Nopporn Kaiyawet | Thanyada Rungrotmongkol | Supot Hannongbua | T. Rungrotmongkol | S. Hannongbua | Nopporn Kaiyawet
[1] Jan H. Jensen,et al. Very fast prediction and rationalization of pKa values for protein–ligand complexes , 2008, Proteins.
[2] J. Aqvist,et al. A new method for predicting binding affinity in computer-aided drug design. , 1994, Protein engineering.
[3] Chris Oostenbrink,et al. Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations , 2012, J. Chem. Inf. Model..
[4] R M Stroud,et al. Atomic structure of thymidylate synthase: target for rational drug design. , 1987, Science.
[5] Ray Luo,et al. Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers. , 2010, Journal of chemical theory and computation.
[6] D. Matthews,et al. Stereochemical mechanism of action for thymidylate synthase based on the X-ray structure of the covalent inhibitory ternary complex with 5-fluoro-2'-deoxyuridylate and 5,10-methylenetetrahydrofolate. , 1990, Journal of molecular biology.
[7] R. Stroud,et al. Plastic adaptation toward mutations in proteins: Structural comparison of thymidylate synthases , 1990, Proteins.
[8] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[9] B. Honig,et al. Classical electrostatics in biology and chemistry. , 1995, Science.
[10] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[11] Urban Bren,et al. Individual degrees of freedom and the solvation properties of water. , 2012, The Journal of chemical physics.
[12] T. Darden,et al. The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods , 1993 .
[13] P. Danenberg. Thymidylate synthetase - a target enzyme in cancer chemotherapy. , 1977, Biochimica et biophysica acta.
[14] Urban Bren,et al. Decomposition of the solvation free energies of deoxyribonucleoside triphosphates using the free energy perturbation method. , 2006, The journal of physical chemistry. B.
[15] P. Cieplak,et al. The effect of 5-substitution in the pyrimidine ring of dUMP on the interaction with thymidylate synthase: molecular modeling and QSAR. , 2007, Bioorganic & medicinal chemistry.
[16] R. Raines,et al. Kinetics and thermodynamics of the interaction of 5-fluoro-2'-deoxyuridylate with thymidylate synthase. , 1987, Biochemistry.
[17] K. Sharp,et al. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .
[18] P. Schultz,et al. Trapping of the C5 Methylene Intermediate in Thymidylate Synthase , 1998 .
[19] A. Hamza,et al. Understanding microscopic binding of human microsomal prostaglandin E synthase-1 (mPGES-1) trimer with substrate PGH2 and cofactor GSH: insights from computational alanine scanning and site-directed mutagenesis. , 2010, The journal of physical chemistry. B.
[20] R. Stroud,et al. Stereochemistry of a multistep/bipartite methyl transfer reaction: thymidylate synthase , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[21] Urban Bren,et al. Microwave catalysis through rotationally hot reactive species. , 2008, The journal of physical chemistry. A.
[22] Urban Bren,et al. DNA duplex stability: the role of preorganized electrostatics. , 2010, The journal of physical chemistry. B.
[23] J. E. Villafranca,et al. Kinetic scheme for thymidylate synthase from Escherichia coli: determination from measurements of ligand binding, primary and secondary isotope effects, and pre-steady-state catalysis. , 1997, Biochemistry.
[24] Swapnil Chavan,et al. Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2) , 2012, Molecular Diversity.
[25] Gregory D. Hawkins,et al. Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium , 1996 .
[26] M. Moore,et al. Trapping and partial characterization of an adduct postulated to be the covalent catalytic ternary complex of thymidylate synthase. , 1986, Biochemistry.
[27] P. Schultz,et al. Tyrosine 146 of thymidylate synthase assists proton abstraction from the 5-position of 2'-deoxyuridine 5'-monophosphate. , 1999, Biochemistry.
[28] P. Schultz,et al. A MODEL FOR HYDRIDE TRANSFER IN THYMIDYLATE SYNTHASE BASED ON UNNATURAL AMINO ACID MUTAGENESIS , 1999 .
[29] Gregory D. Hawkins,et al. Pairwise solute descreening of solute charges from a dielectric medium , 1995 .
[30] Jan H. Jensen,et al. Very fast empirical prediction and rationalization of protein pKa values , 2005, Proteins.
[31] D. Santi,et al. The catalytic mechanism and structure of thymidylate synthase. , 1995, Annual review of biochemistry.
[32] D. Santi. Perspective on the design and biochemical pharmacology of inhibitors of thymidylate synthetase. , 1980, Journal of medicinal chemistry.
[33] Urban Bren,et al. Do all pieces make a whole? Thiele cumulants and the free energy decomposition , 2007 .
[34] A. Warshel,et al. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. , 1992, Protein engineering.
[35] Y. Cheng,et al. Metabolism and mechanism of action of 5-fluorouracil. , 1990, Pharmacology & therapeutics.
[36] D. Case,et al. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. , 2003, Journal of molecular biology.
[37] Ray Luo,et al. On removal of charge singularity in Poisson-Boltzmann equation. , 2009, The Journal of chemical physics.